data_3Q50 # _entry.id 3Q50 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3Q50 pdb_00003q50 10.2210/pdb3q50/pdb NDB NA0896 ? ? RCSB RCSB063201 ? ? WWPDB D_1000063201 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3GCA 'Crystal structure of PreQ1 riboswitch with PreQ0 metabolite bound' unspecified PDB 3Q51 . unspecified # _pdbx_database_status.entry_id 3Q50 _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-12-26 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Jenkins, J.L.' 1 'Krucinska, J.' 2 'Wedekind, J.E.' 3 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation.' J.Biol.Chem. 286 24626 24637 2011 JBCHA3 US 0021-9258 0071 ? 21592962 10.1074/jbc.M111.230375 1 'The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain.' J.Biol.Chem. 284 11012 11016 2010 JBCHA3 US 0021-9258 0071 ? 19261617 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Jenkins, J.L.' 1 ? primary 'Krucinska, J.' 2 ? primary 'McCarty, R.M.' 3 ? primary 'Bandarian, V.' 4 ? primary 'Wedekind, J.E.' 5 ? 1 'Spitale, R.C.' 6 ? 1 'Torelli, A.T.' 7 ? 1 'Krucinska, J.' 8 ? 1 'Bandarian, V.' 9 ? 1 'Wedekind, J.E.' 10 ? # _cell.entry_id 3Q50 _cell.length_a 110.782 _cell.length_b 110.782 _cell.length_c 59.605 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3Q50 _symmetry.space_group_name_H-M 'P 63 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'PREQ1 RIBOSWITCH' 10599.417 1 ? ? ? ? 2 non-polymer syn 7-DEAZA-7-AMINOMETHYL-GUANINE 179.179 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 4 ? ? ? ? 4 water nat water 18.015 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG _entity_poly.pdbx_seq_one_letter_code_can CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 U n 1 3 G n 1 4 G n 1 5 G n 1 6 U n 1 7 C n 1 8 G n 1 9 C n 1 10 A n 1 11 G n 1 12 U n 1 13 A n 1 14 A n 1 15 C n 1 16 C n 1 17 C n 1 18 C n 1 19 A n 1 20 G n 1 21 U n 1 22 U n 1 23 A n 1 24 A n 1 25 C n 1 26 A n 1 27 A n 1 28 A n 1 29 A n 1 30 C n 1 31 A n 1 32 A n 1 33 G n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'The RNA strand was chemically synthesized based on the sequence of class I, Type 1 PreQ1 riboswitch aptamer from T. Tengcongensis' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3Q50 _struct_ref.pdbx_db_accession 3Q50 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3Q50 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 33 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3Q50 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 33 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 33 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 PRF non-polymer . 7-DEAZA-7-AMINOMETHYL-GUANINE ? 'C7 H9 N5 O' 179.179 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 3Q50 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.98 _exptl_crystal.density_percent_sol 75.30 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.6 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '1.8 M Li2SO4, 0.05 M MES pH 5.6, and 0.01 M MgCl2(H20)6, vapor diffusion, hanging drop, temperature 293K' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.pdbx_collection_date 2009-11-09 _diffrn_detector.details 'Rh coated Si vertical focus mirror' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Horizontal focusing 5.05 asymmetric cut Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9769 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'CHESS BEAMLINE A1' _diffrn_source.pdbx_synchrotron_site CHESS _diffrn_source.pdbx_synchrotron_beamline A1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9769 # _reflns.entry_id 3Q50 _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 25.000 _reflns.d_resolution_high 2.7250 _reflns.number_obs 6041 _reflns.number_all ? _reflns.percent_possible_obs 98.700 _reflns.pdbx_Rmerge_I_obs 0.077 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 16.400 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.500 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_unique_obs _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.750 2.800 94.800 0.586 ? ? 5.100 ? ? ? ? ? ? 1 1 2.800 2.850 99.300 0.602 ? ? 5.500 ? ? ? ? ? ? 2 1 2.850 2.900 99.000 0.452 ? ? 6.100 ? ? ? ? ? ? 3 1 2.900 2.960 100.000 0.359 ? ? 6.100 ? ? ? ? ? ? 4 1 2.960 3.030 100.000 0.232 ? ? 6.400 ? ? ? ? ? ? 5 1 3.030 3.100 100.000 0.187 ? ? 6.700 ? ? ? ? ? ? 6 1 3.100 3.170 100.000 0.135 ? ? 6.700 ? ? ? ? ? ? 7 1 3.170 3.260 100.000 0.114 ? ? 7.000 ? ? ? ? ? ? 8 1 3.260 3.360 99.300 0.102 ? ? 6.800 ? ? ? ? ? ? 9 1 3.360 3.460 100.000 0.091 ? ? 6.900 ? ? ? ? ? ? 10 1 3.460 3.590 99.300 0.097 ? ? 6.800 ? ? ? ? ? ? 11 1 3.590 3.730 99.400 0.086 ? ? 6.800 ? ? ? ? ? ? 12 1 3.730 3.900 99.700 0.093 ? ? 6.900 ? ? ? ? ? ? 13 1 3.900 4.100 99.000 0.082 ? ? 6.800 ? ? ? ? ? ? 14 1 4.100 4.360 98.700 0.083 ? ? 6.800 ? ? ? ? ? ? 15 1 4.360 4.690 98.700 0.071 ? ? 6.700 ? ? ? ? ? ? 16 1 4.690 5.160 99.300 0.073 ? ? 6.600 ? ? ? ? ? ? 17 1 5.160 5.900 98.800 0.060 ? ? 6.500 ? ? ? ? ? ? 18 1 5.900 7.400 98.800 0.055 ? ? 6.300 ? ? ? ? ? ? 19 1 7.400 25.000 91.400 0.041 ? ? 5.800 ? ? ? ? ? ? 20 1 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3Q50 _refine.ls_number_reflns_obs 5712 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.13 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 22.010 _refine.ls_d_res_high 2.750 _refine.ls_percent_reflns_obs 95.86 _refine.ls_R_factor_obs 0.2144 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2104 _refine.ls_R_factor_R_free 0.2522 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.03 _refine.ls_number_reflns_R_free 573 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min 0.500 _refine.occupancy_max 1.000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] 12.6181 _refine.aniso_B[2][2] 12.6181 _refine.aniso_B[3][3] -25.2362 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.247 _refine.solvent_model_param_bsol 32.544 _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 3GCA _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.35 _refine.pdbx_overall_phase_error 23.06 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_overall_ESU_R ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? # _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_analyze.entry_id 3Q50 _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs 0.36 _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 702 _refine_hist.pdbx_number_atoms_ligand 33 _refine_hist.number_atoms_solvent 1 _refine_hist.number_atoms_total 736 _refine_hist.d_res_high 2.750 _refine_hist.d_res_low 22.010 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.007 ? ? 816 'X-RAY DIFFRACTION' ? f_angle_d 1.689 ? ? 1267 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 17.512 ? ? 394 'X-RAY DIFFRACTION' ? f_chiral_restr 0.061 ? ? 164 'X-RAY DIFFRACTION' ? f_plane_restr 0.007 ? ? 34 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.number_reflns_obs 'X-RAY DIFFRACTION' . 2.7501 3.0262 1135 0.3099 88.00 0.3489 . . 132 . . . . 'X-RAY DIFFRACTION' . 3.0262 3.4626 1298 0.2250 99.00 0.2971 . . 144 . . . . 'X-RAY DIFFRACTION' . 3.4626 4.3570 1315 0.2080 99.00 0.2763 . . 144 . . . . 'X-RAY DIFFRACTION' . 4.3570 22.0108 1391 0.1692 98.00 0.1850 . . 153 . . . . # _struct.entry_id 3Q50 _struct.title 'Structural analysis of a class I PreQ1 riboswitch aptamer in the metabolite-bound state' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3Q50 _struct_keywords.text 'PREQ1, PREQ0, RNA, RIBOSOMAL BINDING SITE, APTAMER, METABOLITE, Pseudoknot, H-type, RIBOSWITCH' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 4 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 1 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 1 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 1 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 A A 19 N1 ? ? A U 2 A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 A A 19 N6 ? ? A U 2 A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 18 N3 ? ? A G 3 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 18 O2 ? ? A G 3 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 18 N4 ? ? A G 3 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 17 N3 ? ? A G 4 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 17 O2 ? ? A G 4 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 17 N4 ? ? A G 4 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 16 N3 ? ? A G 5 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 5 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 5 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 5 N2 ? ? ? 1_555 A A 27 N1 ? ? A G 5 A A 27 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog16 hydrog ? ? A G 5 N3 ? ? ? 1_555 A A 27 N6 ? ? A G 5 A A 27 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog17 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 28 N7 ? ? A U 6 A A 28 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog18 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 28 N6 ? ? A U 6 A A 28 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog19 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 11 N7 ? ? A C 7 A G 11 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog20 hydrog ? ? A C 7 O2 ? ? ? 1_555 A A 29 N6 ? ? A C 7 A A 29 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog21 hydrog ? ? A C 7 O2 ? ? ? 1_555 A C 30 N4 ? ? A C 7 A C 30 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog22 hydrog ? ? A G 8 N2 ? ? ? 1_555 A A 31 N1 ? ? A G 8 A A 31 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog23 hydrog ? ? A G 8 N3 ? ? ? 1_555 A A 31 N6 ? ? A G 8 A A 31 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog24 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 33 N1 ? ? A C 9 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 33 O6 ? ? A C 9 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 33 N2 ? ? A C 9 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A A 10 N3 ? ? ? 1_555 A A 32 N6 ? ? A A 10 A A 32 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog28 hydrog ? ? A G 11 N2 ? ? ? 1_555 A A 14 N1 ? ? A G 11 A A 14 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog29 hydrog ? ? A G 11 N3 ? ? ? 1_555 A A 14 N6 ? ? A G 11 A A 14 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog30 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 30 N3 ? ? A G 11 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 30 O2 ? ? A G 11 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 30 N4 ? ? A G 11 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A A 13 N6 ? ? ? 1_555 A A 31 N3 ? ? A A 13 A A 31 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog34 hydrog ? ? A C 16 O2 ? ? ? 1_555 A A 28 N6 ? ? A C 16 A A 28 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog35 hydrog ? ? A C 17 O2 ? ? ? 1_555 A A 26 N6 ? ? A C 17 A A 26 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog36 hydrog ? ? A G 20 N2 ? ? ? 1_555 A U 21 O4 ? ? A G 20 A U 21 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A PRF 34 ? 8 'BINDING SITE FOR RESIDUE PRF A 34' AC2 Software A SO4 101 ? 2 'BINDING SITE FOR RESIDUE SO4 A 101' AC3 Software A SO4 102 ? 3 'BINDING SITE FOR RESIDUE SO4 A 102' AC4 Software A SO4 103 ? 3 'BINDING SITE FOR RESIDUE SO4 A 103' AC5 Software A SO4 104 ? 4 'BINDING SITE FOR RESIDUE SO4 A 104' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 8 G A 5 ? G A 5 . ? 1_555 ? 2 AC1 8 U A 6 ? U A 6 . ? 1_555 ? 3 AC1 8 G A 11 ? G A 11 . ? 1_555 ? 4 AC1 8 C A 15 ? C A 15 . ? 1_555 ? 5 AC1 8 C A 16 ? C A 16 . ? 1_555 ? 6 AC1 8 A A 29 ? A A 29 . ? 1_555 ? 7 AC1 8 C A 30 ? C A 30 . ? 1_555 ? 8 AC1 8 SO4 C . ? SO4 A 101 . ? 1_555 ? 9 AC2 2 G A 11 ? G A 11 . ? 1_555 ? 10 AC2 2 PRF B . ? PRF A 34 . ? 1_555 ? 11 AC3 3 C A 15 ? C A 15 . ? 1_555 ? 12 AC3 3 C A 16 ? C A 16 . ? 1_555 ? 13 AC3 3 C A 17 ? C A 17 . ? 1_555 ? 14 AC4 3 C A 17 ? C A 17 . ? 1_555 ? 15 AC4 3 C A 18 ? C A 18 . ? 1_555 ? 16 AC4 3 A A 19 ? A A 19 . ? 1_555 ? 17 AC5 4 U A 12 ? U A 12 . ? 10_665 ? 18 AC5 4 U A 12 ? U A 12 . ? 1_555 ? 19 AC5 4 A A 13 ? A A 13 . ? 1_555 ? 20 AC5 4 A A 32 ? A A 32 . ? 1_555 ? # _atom_sites.entry_id 3Q50 _atom_sites.fract_transf_matrix[1][1] 0.009027 _atom_sites.fract_transf_matrix[1][2] 0.005212 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.010423 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.016777 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 C 1 1 1 C C A . n A 1 2 U 2 2 2 U U A . n A 1 3 G 3 3 3 G G A . n A 1 4 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 G 8 8 8 G G A . n A 1 9 C 9 9 9 C C A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 U 12 12 12 U U A . n A 1 13 A 13 13 13 A A A . n A 1 14 A 14 14 14 A A A . n A 1 15 C 15 15 15 C C A . n A 1 16 C 16 16 16 C C A . n A 1 17 C 17 17 17 C C A . n A 1 18 C 18 18 18 C C A . n A 1 19 A 19 19 19 A A A . n A 1 20 G 20 20 20 G G A . n A 1 21 U 21 21 21 U U A . n A 1 22 U 22 22 22 U U A . n A 1 23 A 23 23 23 A A A . n A 1 24 A 24 24 24 A A A . n A 1 25 C 25 25 25 C C A . n A 1 26 A 26 26 26 A A A . n A 1 27 A 27 27 27 A A A . n A 1 28 A 28 28 28 A A A . n A 1 29 A 29 29 29 A A A . n A 1 30 C 30 30 30 C C A . n A 1 31 A 31 31 31 A A A . n A 1 32 A 32 32 32 A A A . n A 1 33 G 33 33 33 G G A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 PRF 1 34 34 PRF PRF A . C 3 SO4 1 101 101 SO4 SO4 A . D 3 SO4 1 102 102 SO4 SO4 A . E 3 SO4 1 103 103 SO4 SO4 A . F 3 SO4 1 104 104 SO4 SO4 A . G 4 HOH 1 200 200 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id SO4 _pdbx_struct_special_symmetry.auth_seq_id 104 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id F _pdbx_struct_special_symmetry.label_comp_id SO4 _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2011-05-18 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2013-06-12 4 'Structure model' 1 3 2018-01-24 5 'Structure model' 1 4 2023-09-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Structure summary' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 5 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' audit_author 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' pdbx_initial_refinement_model 6 5 'Structure model' pdbx_struct_special_symmetry 7 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_audit_author.name' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SCALEPACK . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 2 PHENIX 1.6_289 ? package 'Paul D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 3 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 4 HKL-2000 . ? ? ? ? 'data collection' ? ? ? 5 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 6 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? 7 PHENIX 1.6_289 ? ? ? ? phasing ? ? ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C3'" A U 12 ? ? "O3'" A U 12 ? ? P A A 13 ? ? 127.25 119.70 7.55 1.20 Y 2 1 C8 A A 13 ? ? N9 A A 13 ? ? C4 A A 13 ? ? 103.27 105.80 -2.53 0.40 N 3 1 "C3'" A C 15 ? ? "O3'" A C 15 ? ? P A C 16 ? ? 112.38 119.70 -7.32 1.20 Y 4 1 "C3'" A C 16 ? ? "O3'" A C 16 ? ? P A C 17 ? ? 111.83 119.70 -7.87 1.20 Y # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 PRF N1 N N N 114 PRF C2 C N N 115 PRF N3 N N N 116 PRF C4 C Y N 117 PRF C5 C Y N 118 PRF C6 C N N 119 PRF O6 O N N 120 PRF C7 C Y N 121 PRF C10 C N N 122 PRF N11 N N N 123 PRF C8 C Y N 124 PRF N9 N Y N 125 PRF N2 N N N 126 PRF H91 H N N 127 PRF H101 H N N 128 PRF H102 H N N 129 PRF H111 H N N 130 PRF H112 H N N 131 PRF H81 H N N 132 PRF HN91 H N N 133 PRF HN21 H N N 134 PRF HN22 H N N 135 SO4 S S N N 136 SO4 O1 O N N 137 SO4 O2 O N N 138 SO4 O3 O N N 139 SO4 O4 O N N 140 U OP3 O N N 141 U P P N N 142 U OP1 O N N 143 U OP2 O N N 144 U "O5'" O N N 145 U "C5'" C N N 146 U "C4'" C N R 147 U "O4'" O N N 148 U "C3'" C N S 149 U "O3'" O N N 150 U "C2'" C N R 151 U "O2'" O N N 152 U "C1'" C N R 153 U N1 N N N 154 U C2 C N N 155 U O2 O N N 156 U N3 N N N 157 U C4 C N N 158 U O4 O N N 159 U C5 C N N 160 U C6 C N N 161 U HOP3 H N N 162 U HOP2 H N N 163 U "H5'" H N N 164 U "H5''" H N N 165 U "H4'" H N N 166 U "H3'" H N N 167 U "HO3'" H N N 168 U "H2'" H N N 169 U "HO2'" H N N 170 U "H1'" H N N 171 U H3 H N N 172 U H5 H N N 173 U H6 H N N 174 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 PRF N1 C2 sing N N 118 PRF N1 C6 sing N N 119 PRF N1 H91 sing N N 120 PRF C2 N3 doub N N 121 PRF C2 N2 sing N N 122 PRF N3 C4 sing N N 123 PRF C4 C5 doub Y N 124 PRF C4 N9 sing Y N 125 PRF C5 C6 sing N N 126 PRF C5 C7 sing Y N 127 PRF C6 O6 doub N N 128 PRF C7 C10 sing N N 129 PRF C7 C8 doub Y N 130 PRF C10 N11 sing N N 131 PRF C10 H101 sing N N 132 PRF C10 H102 sing N N 133 PRF N11 H111 sing N N 134 PRF N11 H112 sing N N 135 PRF C8 N9 sing Y N 136 PRF C8 H81 sing N N 137 PRF N9 HN91 sing N N 138 PRF N2 HN21 sing N N 139 PRF N2 HN22 sing N N 140 SO4 S O1 doub N N 141 SO4 S O2 doub N N 142 SO4 S O3 sing N N 143 SO4 S O4 sing N N 144 U OP3 P sing N N 145 U OP3 HOP3 sing N N 146 U P OP1 doub N N 147 U P OP2 sing N N 148 U P "O5'" sing N N 149 U OP2 HOP2 sing N N 150 U "O5'" "C5'" sing N N 151 U "C5'" "C4'" sing N N 152 U "C5'" "H5'" sing N N 153 U "C5'" "H5''" sing N N 154 U "C4'" "O4'" sing N N 155 U "C4'" "C3'" sing N N 156 U "C4'" "H4'" sing N N 157 U "O4'" "C1'" sing N N 158 U "C3'" "O3'" sing N N 159 U "C3'" "C2'" sing N N 160 U "C3'" "H3'" sing N N 161 U "O3'" "HO3'" sing N N 162 U "C2'" "O2'" sing N N 163 U "C2'" "C1'" sing N N 164 U "C2'" "H2'" sing N N 165 U "O2'" "HO2'" sing N N 166 U "C1'" N1 sing N N 167 U "C1'" "H1'" sing N N 168 U N1 C2 sing N N 169 U N1 C6 sing N N 170 U C2 O2 doub N N 171 U C2 N3 sing N N 172 U N3 C4 sing N N 173 U N3 H3 sing N N 174 U C4 O4 doub N N 175 U C4 C5 sing N N 176 U C5 C6 doub N N 177 U C5 H5 sing N N 178 U C6 H6 sing N N 179 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3Q50 'double helix' 3Q50 'quadruple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A C 1 1_555 A G 20 1_555 0.205 -0.094 -0.026 -0.323 -2.065 -0.020 1 A_C1:G20_A A 1 ? A 20 ? 19 1 1 A U 2 1_555 A A 19 1_555 -0.164 -0.032 0.215 -0.216 -15.901 1.139 2 A_U2:A19_A A 2 ? A 19 ? 20 1 1 A G 3 1_555 A C 18 1_555 0.187 -0.199 0.266 -9.625 -11.553 -4.123 3 A_G3:C18_A A 3 ? A 18 ? 19 1 1 A G 4 1_555 A C 17 1_555 -0.095 -0.241 0.271 -6.732 -8.125 0.217 4 A_G4:C17_A A 4 ? A 17 ? 19 1 1 A G 5 1_555 A C 16 1_555 0.020 -0.213 -0.111 -6.925 -10.774 -1.891 5 A_G5:C16_A A 5 ? A 16 ? 19 1 1 A U 6 1_555 A A 28 1_555 -0.146 3.487 1.253 -28.198 -17.454 -64.535 6 A_U6:A28_A A 6 ? A 28 ? 23 3 1 A C 7 1_555 A A 29 1_555 4.797 0.191 2.053 -22.665 14.025 -41.227 7 A_C7:A29_A A 7 ? A 29 ? ? ? 1 A G 11 1_555 A C 30 1_555 -0.154 -0.202 0.483 -2.273 -18.057 0.154 8 A_G11:C30_A A 11 ? A 30 ? 19 1 1 A G 8 1_555 A A 31 1_555 3.805 -3.970 -0.800 18.825 12.050 -66.432 9 A_G8:A31_A A 8 ? A 31 ? 10 6 1 A A 10 1_555 A A 32 1_555 6.328 -3.779 -0.730 -6.675 -19.993 -17.153 10 A_A10:A32_A A 10 ? A 32 ? ? 10 1 A G 33 1_555 A C 9 1_555 0.854 -0.212 0.171 -3.654 -6.100 -5.193 11 A_G33:C9_A A 33 ? A 9 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 1 1_555 A G 20 1_555 A U 2 1_555 A A 19 1_555 0.602 -1.776 3.021 0.650 8.868 29.732 -4.774 -1.020 2.415 16.815 -1.232 31.005 1 AA_C1U2:A19G20_AA A 1 ? A 20 ? A 2 ? A 19 ? 1 A U 2 1_555 A A 19 1_555 A G 3 1_555 A C 18 1_555 -0.637 -1.784 3.195 -0.347 11.672 36.912 -3.985 0.924 2.542 17.893 0.532 38.654 2 AA_U2G3:C18A19_AA A 2 ? A 19 ? A 3 ? A 18 ? 1 A G 3 1_555 A C 18 1_555 A G 4 1_555 A C 17 1_555 0.781 -1.872 3.047 2.286 5.296 25.176 -5.496 -1.185 2.663 11.951 -5.157 25.818 3 AA_G3G4:C17C18_AA A 3 ? A 18 ? A 4 ? A 17 ? 1 A G 4 1_555 A C 17 1_555 A G 5 1_555 A C 16 1_555 0.022 -1.694 3.235 4.972 4.495 37.735 -3.122 0.565 3.000 6.884 -7.614 38.304 4 AA_G4G5:C16C17_AA A 4 ? A 17 ? A 5 ? A 16 ? 1 A G 5 1_555 A C 16 1_555 A U 6 1_555 A A 28 1_555 -6.540 -1.060 1.371 11.847 3.923 20.606 -2.374 15.182 -2.180 9.882 -29.846 24.055 5 AA_G5U6:A28C16_AA A 5 ? A 16 ? A 6 ? A 28 ? 1 A U 6 1_555 A A 28 1_555 A C 7 1_555 A A 29 1_555 3.002 -1.344 3.649 3.669 1.172 51.963 -1.620 -3.139 3.809 1.335 -4.181 52.096 6 AA_U6C7:A29A28_AA A 6 ? A 28 ? A 7 ? A 29 ? 1 A C 7 1_555 A A 29 1_555 A G 11 1_555 A C 30 1_555 -0.962 1.746 0.696 148.564 93.877 -161.715 -0.902 -0.435 0.668 -46.953 74.305 -179.323 7 AA_C7G11:C30A29_AA A 7 ? A 29 ? A 11 ? A 30 ? 1 A G 11 1_555 A C 30 1_555 A G 8 1_555 A A 31 1_555 -2.851 2.825 3.034 -170.742 -10.978 -116.071 -1.375 -2.026 1.170 5.532 -86.043 -175.289 8 AA_G11G8:A31C30_AA A 11 ? A 30 ? A 8 ? A 31 ? 1 A G 8 1_555 A A 31 1_555 A A 10 1_555 A A 32 1_555 -5.186 1.603 -2.536 161.345 55.500 -6.877 -1.063 -1.849 4.222 -29.183 84.839 -170.641 9 AA_G8A10:A32A31_AA A 8 ? A 31 ? A 10 ? A 32 ? 1 A A 10 1_555 A A 32 1_555 A G 33 1_555 A C 9 1_555 -0.630 -4.224 0.026 147.552 -92.058 72.432 -1.924 0.619 1.387 -46.687 -74.831 175.091 10 AA_A10G33:C9A32_AA A 10 ? A 32 ? A 33 ? A 9 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 7-DEAZA-7-AMINOMETHYL-GUANINE PRF 3 'SULFATE ION' SO4 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3GCA _pdbx_initial_refinement_model.details ? #